MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b1982 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.451313 (mmol/gDw/h)
  Minimum Production Rate : 1.729859 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.621902
  EX_nh4_e : 13.523939
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.435339
  EX_so4_e : 0.113650
  EX_k_e : 0.088093
  EX_fe2_e : 0.007249
  EX_mg2_e : 0.003915
  EX_ca2_e : 0.002349
  EX_cl_e : 0.002349
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.612152
  EX_co2_e : 21.124488
  EX_h_e : 15.187369
  EX_ac_e : 2.389921
  Auxiliary production reaction : 1.729859
  DM_oxam_c : 0.000505
  DM_5drib_c : 0.000303
  EX_glyclt_e : 0.000302
  DM_4crsol_c : 0.000101

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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